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Four thousand years prior to the the main events of the Sonic the Hedgehog series, the Knuckles ClanEchidnas ruled a city on the site of what would become Mystic Ruins. The Clan chieftain, Pachacamac, attempted to remove the Chaos Emeralds from the ancient Chao shrine on the outskirts of the city. This angered their guardian, Chaos, who destroyed almost the entire Knuckles Clan civilization in vengeance. The chaos energy backlash from Chaos' attack lifted the Emerald Shrine (along with a vast chunk of land) out of the ground: producing Angel Island. The few surviving Knuckles Clan Echidnas, stranded on this floating landmass, went into terminal decline–Knuckles himself being the last descendant of this once-great civilization.

Some remnants of the echidna city remained on the surface, where they were gradually overrun by the encroaching jungle flora. It is this swampy, ruin-studded rainforest which forms the modern-day Mystic Ruins.

The Mystic Ruins first appeared in Sonic Adventure as an Adventure Field. In this game, a group of archaeologists have gone to the Mystic Ruins to explore those ruins of the Knuckles Clan's city which remained on the planet's surface. Unfortunately, they were not prepared for the crash landing of Angel Island. Some of the archaeologists have gotten themselves lost in the maze of the thick jungle that surrounds the Maya-like temple, while the others who had stayed behind, near the Mystic Ruins Train Station, built a log cabin to make camp. The archaeologists who built camp are constantly worried about there friends but are to afraid to go in to find them. If Sonic, Tails, and Friends find any of the archaeologists that are lost in the forest they will state that they can't find the ancient temple or their way out, they however kindly refuse the help of the heroes saying it wouldn't be very adventurous. (possibly a play on the title of the game, Sonic Adventure)

Tails's workshop/house can also be found in Mystic Ruins. A train station has also been built, to serve the archaeological sites. During the events of Sonic Adventure, Angel Island crashed back to the surface of the planet, on the shoreline next to Mystic Ruins; but it floated away again after the Master Emerald was restored.

The main area is large grassy plateau with some buildings and trees. One side leads to a steep cliff into the ocean, and on the other side is a mountain with various caves. A hill is located in the eastern part of it.

Train station - A tall wooden building with stairs that leads to a stone bridge where the train waits for passengers to take to Station Square. Inside the building is a ladder that leads to a raft that takes people to the Egg Carrier.

Tails' Workshop - A small two-story house located on a hill. It has with a long biplane runway with two rows of palm trees leading out into the ocean. The workshop is apparently connected to a cave beneath the house, where Tails works on his Tornado 2.

Lake - A small lake with a waterfall leading to it and a river leading into the ocean. A Silver Chao Egg can be discovered by pushing against a panel.

Caves - The west caves lead to Angel Island. The east caves lead to an upgrade for Knuckles and the Mystic Ruins Chao Garden.

Chao Garden - A large grassy area on the side of a mountain. There is a lake and several large rocks lying about. The lake is connected to a larger one which is above the waterfall, it is there where Chaos 4 was fought.

Windy Valley - A windy Action Stage where tornadoes easily form. The second part of the stage consists of floating paths high above the clouds.

Echidna Temple - A large mayan-like temple that used to be the holy site of the Echidnas. It is the portal to Lost World.

Lost World - An Action Stage set inside the temple. It is extremely large, and one part somehow features an outside section that looks nothing like the jungle. The temple also contains various booby traps such as a giant rolling stone ball and gravity panels that move on the wall. The center of the temple contains a mural of Perfect Chaos.

Sand Hill - A long desert slope with various ruins which burst from the ground. (Could be Sandopolis as it's in the direction of Angel Island.)

Final Egg - Eggman's large tower base, where he keeps his Egg Carrier and Egg Viper. It is entered via a long tube in the jungle, this is the base that the first of the E-100 series was created. The base is heavily defended and has three sectors, the first is simple pathways with spinning iron, spike balls and grinding mechanisms. The second drastically changes from the first, it is basically a large shaft that leads downwards, three tunnels lead to different levels and at the bottom there are more spinning masses. The last is similar to the first, except for three large rooms containing exploding crabs as well as pitfalls.

After Angel Island crashes in Mystic Ruins, most characters can access the island via a windy cave. The main area is a long corridor that leads to a large area where the Master Emerald can be found.

Master Emerald Altar - The ancient altar where the broken Master Emerald is, the altar is now broken and worn down due to extreme age. The Altar now stands on a small piece of ground which is separated from the rest of the island. Only by flying or using a wooden bridge, which was apparently built by Knuckles, can the altar be reached

Ice Cave - A frozen cave with a lake that leads to Ice Cap.

Ice Cap - A cold, snowy mountain with many caves which contains a frozen lake and a large number of satellites. The second part of the stage consists of a long hill for snowboarding. The slope is used for skiing. May have been inspired by Ice Cap Zone of Sonic the Hedgehog 3.

Red Mountain - Another mountain of Angel Island, except this one is volcanic. It is surrounded by smaller mountains–most of them are connected by metal bridges. There is also a large network of underground tunnels and caves which are flooded with lava. The second section may have been inspired by Sonic & KnucklesLava Reef Zone.

Tikal has the power to show the Mystic Ruins to others during her lifetime when her people lived. Whether this is an illusion or actual time travel is unknown, as characters can talk to the local echidnas and Tails even finds his Rhythm Badge here.

City - A great city where the warrior echidnas live. The whole city is surrounded by mountains with the "back" of the city facing the great jungle. The city is Aztec or Mayan in appearance, and in modern times, the city has been lost to the jungle, with only the center pyramid temple to the Lost World remaining. Before its ruin, it was ruled by Chief Pachacamac. Sonic is the only one who cannot visit this place, since, when Tikal teleports Sonic, he was shown in the battle section of when Pachacamac was killed.

Bridge - The only exit to the city is a cave, at the end of which is a great stone bridge that leads up to the altar. Most of this bridge is left over during modern times as part of Angel Island.

Master Emerald Altar - While still just as old, it is not in ruin as the altar will be on Angel Island. The seven surrounding pillars hold the Chaos Emeralds with the Master Emerald at its center. The altar also has water flowing from it; whether this is a fountain or something magical is unknown. The guardian at the time was Chaos and the environment was suitable for Chao to live as well.

Mystic Ruins now hosts one of Doctor Robotnik's abandoned bases. Said base has been taken over by the Nocturnus forces, who are using it as a prison to hold Knuckles captive. In Sonic Chronicles: The Dark Brotherhood, the Mystic Ruins again features as a game area, although the characters visit a more swamp-like section than those seen in Sonic Adventure. Mystic Ruins is home to many wild animals, such as Queen Wasps, Giant Millipedes and Colossal Worms. Toxic, malodorous gases are emitted into the air by Nocturnus forces, in a bid to clear the area of G.U.N. soldiers. The gas is only passable by Big the Cat.

Later, Shadow the Hedgehog can be seen here when you begin your search for Dr. Eggman, and also unintentionally helps you on your quest in Chapter 3.

Mystic Ruins was seen in "A Chaotic Day", Knuckles finds the police in Casinopolis, and a policeman says it was a glowing object that fell from the sky, Knuckles and the police go inside and look, and find a piece of the Master Emerald. Knuckles picks the Emerald Shard up, but is transported to a version of Mystic Ruins 4000 years ago. Knuckles walks around and finds a echidna named Tikal with her father, Pachacamac. Tikal begs her father not to seize the Chaos Emeralds, but as her father ignores her.

In Sonic Chronicles: The Dark Brotherhood, the BGM for the Mystic Ruins is a remix of the BGM of the Final Fight Zone from Sonic 3D.

In Sonic Adventure, if the temple in the center of the jungle area is approached from outside its render distance at high enough speed, one can see the stone sphere on the left side transforms into a statue of an Echidna whenever it is loaded. The sphere on the right is broken, so its ability to transform if any is unknown.